millironx/SequenceVariation.jl
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Update API documentation for different translate methods

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This commit is contained in:
Thomas A. Christensen II 2023-01-05 13:10:24 -06:00
parent 6a4a39c859
commit ecaa995d2b
2 changed files with 6 additions and 3 deletions
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docs/src/api.md
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@ -22,6 +22,7 @@ Haplotype
reference(::Haplotype)
variations
reconstruct
translate(::Haplotype{S,T}, ::PairwiseAlignment{S,S}) where {S,T}
```
## Variations
@ -30,7 +31,7 @@ reconstruct
Variation
reference(::Variation)
mutation
translate
translate(::Variation{S,T}, ::PairwiseAlignment{S,S}) where {S,T}
refbases
altbases
```

6
docs/src/variations.md
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@ -54,13 +54,15 @@ variations(bos_human_haplotype)
## Reference switching
An individual variation can be mapped to a new reference sequence given an
alignment between the new and old references using the [`translate`](@ref).
alignment between the new and old references using the
[`translate`](@ref translate(::Variation{S,T}, ::PairwiseAlignment{S,S}) where {S,T})
function.
```@repl call_variants
ovis_human_alignment =
PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine)
human_variation = first(variations(bos_ovis_haplotype))
reference(ans) == bovine
SequenceVariation.translate(human_variation, ovis_human_haplotype)
SequenceVariation.translate(human_variation, ovis_human_alignment)
reference(ans) == bovine
```